I'm not sure if you're having the same problem as I am, but I'm having issue with the "Use custom DNS servers" option to override the DNS servers provided by my WAN DHCP lease.
Verizon hijacks bad DNS lookups for their advertising page, and you have to override the DNS servers to disable this "feature". When I do this, the old DNS servers still seem to be honored, and the ad page is still served for bad DNS lookups.
I have traced the problem to /tmp/resolv.conf.auto which seems to APPEND the "Use custom DNS servers" to the existing ones provided by the DHCP lease, rather than replace them. My /tmp/resolv.conf.auto file winds up with 4 DNS servers, the two provided by the DHCP lease, and the my two custom overrides.
I'm not sure if I'm doing something wrong, or if the "custom DNS" functionality isn't working quite right, and appending rather than replacing dns server entries.